Herbaceous data

Last updated: 2021-10-14

Checks: 6 1

Knit directory: ABRPweb/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: uncommitted changes

The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20210616)

The command set.seed(20210616) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: 12d2503

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 12d2503. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .Rproj.user/

Unstaged changes:
    Modified:   analysis/herbData.Rmd
    Modified:   data/perGrass.csv
    Modified:   toDoNotes.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/herbData.Rmd) and HTML (docs/herbData.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
html	0970d10	rswaty	2021-10-13	“final”? files :)
Rmd	1e12644	rswaty	2021-10-13	finalizing datasets
Rmd	344c49e	rswaty	2021-10-13	added perGrass compiled PDF, fixed perGrass
html	9441ffc	rswaty	2021-08-02	Build site.
html	dea6157	rswaty	2021-08-02	Build site.
html	45666af	rswaty	2021-08-02	Build site.
Rmd	527bb38	rswaty	2021-08-02	Added herb and LANDFIRE pages

Herbaceous Data

Data cleaning notes

All cleaned Herbaceous data saved as “herbWU.csv”
For Perennial Grasses, that data was copied and pasted into a new spreadsheet, “perGrass.csv”. Used Pivot Table to create this new spreadsheet.
Assumed “99999” meant “no data”. Changed to “NA”. Looks like (at least for some years) only one quadrat was sampled for % PG, % WP, % OP, % LI AND % BG.
Did nothing with blank cells.
Deleted rows with AVERAGES
- Bull-dozing happened (instead of fire?) for MONYEAR 2007, B-Ps 7_8, 7_7, 7_6, and 7_4. Did not transfer this information to LASTBURNYEAR (but is is in LASTBURN column). Swaty did not want to mix numerical and text data types in the LASTBURNYEAR column.
In perGrass.csv:
- deleted 21_4 data for 2001
- deleted 40_10 data for 1998
- recalculated average and standard dev for 2010, BP 7_1
- fixed missing years for BP 7_1
- recalculated average and st. deviation for 40_2 (there were multiples)

Perennial Grass Data Table

The cleaned Perennial data is served up below.

All Herbaceious Data Table